Transferring data between Citra builds?

Hey guys, I’m new to using Citra, & I was wondering how game progress is saved when downloading the latest nightly builds. Does game data automatically transfer onto the latest version when it is downloaded?

Yes. All Citra nightly and bleeding edge version saves should be here:

User folder / AppData / Roaming / Citra / sdmc / Nintendo 3DS / 000… / 000… / title